Why is it that with old computer stuff, that the main box or cards, cables, manuals, software seems to nearly always go in separate directions?

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A common reason is the following sequence: The last person with knowledge about the setup leaves a lab/school/company. The setup might still be in use, until something breaks or the setup has to be moved. Afterwards no one is able to redo the wiring and everything will be discarded with proper waste separation.
Sorry, no idea how to avoid this.